Background: Environmental and lifestyle factors such as breast-feeding and pets seem to affect atopic disease prevalence. We identified risk factors for allergic diseases. Methods: We prospectively followed until the age of 5 years a cohort of 1,223 children born into allergic families, who participated in a randomized placebo-controlled trial of probiotics as preventive against allergic disease. We evaluated the cumulative incidence of allergic diseases with questionnaires and examined all children at the ages of 2 and 5 years. Results: Compared to allergy in one parent only, allergy in both parents conferred an increased risk of allergic disease at the ages of 2 (OR 1.64; 95% CI 1.11–2.42, p = 0.013) and 5 (OR 1.83; 95% CI 1.24–2.70, p = 0.002) and at the age of 2 for eczema (OR 1.74; 95% CI 1.17–2.58, p = 0.006). Exclusive breast-feeding over 2 months elevated the risk of eczema at the ages of 2 (OR 1.73; 95% CI 1.15–2.61, p = 0.009) and 5 (OR 1.51; 95% CI 1.03–2.23, p = 0.036). Cat or dog exposure at 0–2 years and at 0–5 years protected against IgE sensitization until 5 years of age (OR 0.60; 95% CI 0.37–1.00, p = 0.048, and OR 0.61; 95% CI 0.39–0.96, p = 0.033), and exposure at the ages of 0–5 years protected against allergic rhinitis until the age of 5 (OR 0.46; 95% CI 0.25–0.85, p = 0.013) in the probiotic group. Conclusions: Allergy in both parents is an independent predictor of eczema and of allergic disease until the ages of 2 and 5. Long, exclusive breast-feeding was associated with increased eczema at the ages of 2 and 5, and cat or dog exposure was associated with decreased IgE sensitization and allergic rhinitis in the probiotic group.